CN111798926B - Pathogenic gene locus database and establishment method thereof - Google Patents
Pathogenic gene locus database and establishment method thereof Download PDFInfo
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/10—Ploidy or copy number detection
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/50—Mutagenesis
Abstract
The invention relates to a pathogenic gene locus database and an establishment method thereof, belonging to the technical field of disease gene detection. The establishment method of the pathogenic gene locus database comprises the following steps: acquiring clinical verified pathogenic gene locus data information as reference data; acquiring a pathogenic gene locus due to amino acid change in the reference data, and expanding codons of amino acids at the locus; acquiring a pathogenic gene locus in the reference data due to change of a shearing locus, and expanding other mutation forms of the locus; screening the data, removing sites with mutation occurrence frequency higher than a preset threshold value, and combining the rest high-risk pathogenic mutation sites and high-risk pathogenic shearing sites with the reference data to form the pathogenic gene site database. The database records a large number of site records with high risk of pathogenicity, can reduce the possibility of omission, and greatly improves the accuracy and efficiency of clinical interpretation work.
Description
Technical Field
The invention relates to the technical field of disease gene detection, in particular to a pathogenic gene locus database and an establishment method thereof.
Background
Gene mutation distinguishes polymorphism and pathogenicity, and about 400 ten thousand mutations exist on the genome of each person, wherein most of the mutations are normal non-pathogenic sites, namely polymorphic sites, and the pathogenic sites are required to be verified by a complex flow, and are a long-term accumulation process.
At present, a plurality of databases for recording pathogenicity sites, such as HGMD, clinVar and the like, but all the databases record mutations which are actually generated, namely the mutations supported by real sample cases, are obtained after comparison and verification with clinical symptoms, namely the most common sites recorded in the databases.
In practice, it is not shown in the database because it is difficult to collect a sufficient sample size of unusual sites for the study of pathogenicity, but because of the diversity of gene mutations and disease symptom relationships (different mutations of the same gene may cause different symptoms) and heterogeneity (one symptom may be caused by a plurality of different gene mutations), the currently found pathogenic sites are very low, i.e., the significance of many mutations is unknown, and although these single rare sites are rare, their total amount is high.
The data with unvalified meanings plays a very important role in prompting the detection of pathogenic gene mutation, and if the gene detection is carried out only by relying on common sites recorded in a database, a plurality of meaningful sites are ignored, so that the influence on the genes with complex heterozygosity pathogeny is very large, the difficulty of detection work is greatly increased, and the diagnosis efficiency is reduced.
Disclosure of Invention
In view of the above, it is necessary to provide a database of pathogenic gene loci that can mine unverified high risk loci for later use and can make it easier for an analyst to find the presence of such loci by increasing the risk weights of the loci when analyzing the detected mutation loci, thereby reducing the detection difficulty and improving the diagnostic efficiency.
A method for establishing a pathogenic gene locus database comprises the following steps:
acquiring reference data: acquiring clinical verified pathogenic gene locus data information as reference data;
expansion yields mutation site data: acquiring pathogenic gene loci in the reference data due to amino acid change, expanding codons of amino acids of the loci, analyzing preset mutation generation conditions, obtaining high-risk pathogenic mutation locus data, and counting for later use;
expansion yields cleavage site data: acquiring pathogenic gene loci in the reference data due to change of the shearing loci, expanding other mutation forms of the loci to obtain high-risk pathogenic shearing locus data, and counting for later use;
extension site screening: and screening the obtained high-risk pathogenic mutation site data and high-risk pathogenic shearing site data, removing sites with mutation occurrence frequency higher than a preset threshold value, and combining the rest high-risk pathogenic mutation sites and high-risk pathogenic shearing sites with the reference data to form the pathogenic gene site database.
The inventor finds in practice that, since all the sites which are found in the database of various pathogenic sites and are generated in the real sample and verified, there are a large number of sites which are related to the sites and have high pathogenic risk, and although the sites with high risk are not verified, the sites can be mined out for later use by the method, so that the detection difficulty is reduced and the diagnosis efficiency is improved.
It will be appreciated that in the step of expanding the data for the mutation site, the amino acid is considered to change the pathogenic gene site, and the core is to consider a single base substitution mutation site, thereby changing the codon of the amino acid, and finally changing the amino acid, thereby causing the disease. Therefore, the preset mutation generation condition is classified and analyzed according to the codon corresponding to the amino acid and the possible condition after single base substitution. If one amino acid corresponds to 3 codons, there may be at most 9 codon patterns in a permutation and combination, and then corresponds to the corresponding amino acid (or stop codon), thereby analyzing the risk of the disease at the evaluation site.
In one embodiment, the reference data is derived from an HGMD database and/or a ClinVar database. It will be appreciated that the reference data sources are not limited, but merely a database that is as authoritative as possible.
In one embodiment, in the step of expanding to obtain mutation site data, the preset mutation generating conditions include the following three types:
the I type mutation is that the amino acid corresponding to the mutated codon is consistent with the reference data;
class II mutation to the post-mutation codon as the stop codon;
class III mutations are those in which the amino acid corresponding to the mutated codon is inconsistent with the reference data and is not a stop codon.
It will be appreciated that the above class III are missense mutations other than class I and class II.
In one embodiment, a class I mutation is determined when both class I and class II mutations are satisfied. It will be appreciated that the same applies to the case of class I and class II, i.e., the case where a mutation in the original database is a termination mutation. So when an extended new mutation is also a termination mutation, it is preferentially judged as class I. It is also understood that class II refers specifically to the fact that in the case where the mutation in the original database is not a termination mutation, the classification defined at the time of termination mutation is extended, and the risk of causing disease in class II is lower than in class I.
In one embodiment, in the step of obtaining the cleavage site data by the extension, the cleavage site extension Is specifically to mutate a mutation site in the reference data to a nucleotide different from the reference data, that Is, an Is mutation.
In one embodiment, in the extended site screening step, the predetermined threshold is 5%. The inventor performs screening and adjustment through the unit large sample data, and finally discovers that 5% is used as a threshold value, so that the method has a good effect, can show possible high risk sites as far as possible, and can avoid reducing risk prompt significance caused by excessive inclusion of nonsensical mutation.
In one embodiment, in the step of screening the extended loci, for loci without a definite occurrence frequency of mutation in the population, and loci obtained by screening that the occurrence frequency of mutation in the population is lower than a predetermined threshold value, the following filtering is performed:
1) Searching a local sample library for a sample with the site, and if the number of samples is smaller than the preset number of samples, reserving the site as a high-risk pathogenic site; if the number of the samples is greater than or equal to the preset number of the samples, judging the sample to be confirmed, and carrying out the next step;
2) And acquiring the clinical information corresponding to the sample to be confirmed, if the clinical information of the sample exceeding the preset proportion is related to the gene function of the site, reserving the site as a high-risk pathogenic site, and if the clinical information of the sample less than or equal to the preset proportion is related to the gene function of the site, rejecting the site.
It will be appreciated that, due to the existence of biological polymorphisms, if all mutations associated with validated mutations are considered as high risk pathogenic loci into the database, this may lead to a reduced meaning of risk cues, and therefore, the initially screened locus data should be filtered, leaving only high risk loci, thereby increasing the value of the invention in establishing a pathogenic genetic locus database.
In one embodiment, the predetermined number of samples is 10 and the predetermined ratio is 1/3. The inventor performs screening and adjustment through the unit large sample data, and finally discovers that the database is built by the parameters, and has better effect.
The invention also discloses a pathogenic gene locus database obtained by the establishment method of the pathogenic gene locus database.
The invention also discloses an automatic pathogenic gene analysis system, which comprises:
the data acquisition module is used for acquiring gene detection data of the sample to be detected;
the data analysis module Is used for substituting the gene detection data into the pathogenic gene locus database for comparison after bioinformatics analysis to obtain information of I type mutation, II type mutation, III type mutation and/or IS type mutation in the sample to be detected;
the judging and outputting module is used for outputting the site mutation information according to the risk level, wherein the risk level is sequentially as follows from high to low: class I mutations, class Is mutations, class II mutations, class III mutations.
Compared with the prior art, the invention has the following beneficial effects:
according to the method for establishing the pathogenic gene locus database, provided by the invention, the pathogenic gene locus data is enriched through mutation expansion of amino acid change and mutation expansion of shearing loci, and then the expanded loci are removed and screened, so that the pathogenic gene locus database which is rich in high-risk pathogenic loci and has a good practical value is finally obtained. Thus making it easier for an analyst to find the presence of these other pathogenic risks associated with validating pathogenic sites, thereby reducing the difficulty of detection and improving diagnostic efficiency.
The pathogenic gene locus database of the invention records a large number of locus records with high pathogenic risk, and can rapidly locate the high-risk pathogenic locus by carrying out matching analysis on the gene detection locus and the locus records, thereby reducing the possibility of omission and greatly improving the accuracy and efficiency of clinical interpretation work.
The pathogenic gene locus database can be used in a pathogenic gene automatic analysis system, and mutation loci possibly having pathogenic risks are all obtained by analysis through an automatic analysis process, so that the requirements on the experience of analysts in the belief generation process are reduced, the detection and analysis difficulty is reduced, and the diagnosis efficiency is improved.
Drawings
FIG. 1 shows amino acid codon table.
Detailed Description
In order that the invention may be readily understood, a more complete description of the invention will be rendered by reference to the appended drawings. Preferred embodiments of the present invention are shown in the drawings. This invention may, however, be embodied in many different forms and should not be construed as limited to the embodiments set forth herein. Rather, these embodiments are provided so that this disclosure will be thorough and complete.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The terminology used herein in the description of the invention is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention. The term "and/or" as used herein includes any and all combinations of one or more of the associated listed items.
The data used in the examples below were collected from the company in daily samples for inspection.
Example 1
A database of pathogenic loci is created by the following method:
1. reference data is acquired.
And obtaining clinically verified pathogenic gene locus data information serving as reference data.
For example, the clinically validated pathogenic gene locus data information may be obtained from databases that record pathogenic loci, such as HGMD, clinVar, etc., and in this embodiment, extended based on the HGMD database.
2. And expanding to obtain mutation site data.
The amino acid changes caused by the base mutation are the most abundant mutation types recorded in a database of pathogenic sites, and the base mutation causing the amino acid changes is often various, some of the amino acid changes need to be mutated into specific amino acid to cause diseases, some of the amino acid changes need to be mutated into stop codon to cause diseases, some of the amino acid changes only need to be changed to cause diseases, but only sites with published research results are recorded in the database. Therefore, the following expansion is performed in the present embodiment:
acquiring pathogenic gene loci due to amino acid changes in the reference data, expanding codons of amino acids at the loci, analyzing preset mutation generation conditions, and classifying all base mutations in one codon into three types of mutations according to the amino acid changes, referring to an amino acid codon table shown in fig. 1:
i, amino acid changes after mutation are consistent with those in a database;
II, a stop codon after mutation;
III, amino acid changes after mutation are inconsistent with and non-stop codons in the database (i.e., missense mutations except for the first two).
When I and II are satisfied simultaneously, the class I mutation is preferentially judged.
Through the process, high-risk pathogenic mutation site data are obtained through expansion, and statistics is carried out for standby.
The DMD genes in the HGMD database are specifically described below as examples:
example one:
if the 268 th amino acid of the DMD gene is Leu, the codon is TTA, and only one record exists in the database, namely [ c.804A > C; leu268Phe ]. Through examination of the codon table, 9 single base mutations can be generated at the codon, and the following mutations are respectively generated:
1) 2 is a termination mutation: [ c.803T > A; leu268term ], [ c.803T > G; leu268term ];
2) 5 are missense mutations: [ c.804A > C; leu268Phe ], [ c.264A > T; leu268Phe ], [ c.803T > C; leu268Ser ] [ c.802T > A; leu268Ile ] [ c.802T > G; leu268Val ];
3) There are 2 synonymous mutations: [ c.804A > G; leu268Leu ], [ c.802T > C; leu268Leu ];
pathogenic mutation site reference data in database with HGMD [ c.804a > C; comparison of Leu268Phe yields, [ c.264A > T; leu268Phe ] is scalable to class I; [ c.803T > A; leu268term ], [ c.803T > G; leu268term ] is scalable to class II; [ c.803T > C; leu268Ser ] [ c.802T > A; leu268Ile ] [ c.802T > G; leu268Val ] is scalable to class III.
Example two:
the 333 rd amino acid of the DMD gene is Ser, the codon is TCA, and only one record exists in the database, namely [ c.998C > A; ser333term ]. Through checking an amino acid codon table, 9 single base mutations at the codon are respectively as follows:
1) There are 2 termination mutations: [ c.998C > A, p.Ser333Term ], [ c.998C > G, p.Ser333Term ];
2) There are 4 missense mutations: [ c.998C > T, p.Ser333Leu ], [ c.997T > C, p.Ser333Pro ], [ c.997T > A, p.Ser333Thr ], [ c.997T > G, p.Ser333Ala ];
3) There are 3 synonymous mutations: [ c.999A > T, p.Ser333ser ], [ c.999A > C, p.Ser333ser ], [ c.999A > G, p.Ser333ser ];
pathogenic mutation site reference data [ c.998c > a in database with HGMD; comparison of p.Ser333term reveals that [ c.998C > G, p.Ser333term ] can be extended to class I or class II, and that class I overlaps class II, i.e., the mutation in the original database is the termination mutation, so that class I is preferentially determined when an extended new mutation is also the termination mutation. Thus, [ c.998C > G, p.Ser333Term ] extends to class I; the 4 missense mutations extend to class III.
3. Expansion yields cleavage site data.
Some base sites at the edges of introns and exons are critical for the cleavage of introns, some introns have other critical cleavage sites in addition to the 4 bases at + -1 and + -2 of the universal introns. Similarly, since only sites from which research results have been published are recorded in the conventional database, the present embodiment expands other mutant forms not recorded in the database into type is based on the coordinates of these key cleavage sites, as follows.
And acquiring pathogenic gene loci in the reference data due to the change of the shearing loci, expanding other mutation forms of the loci to obtain high-risk pathogenic shearing locus data, and counting for later use.
The DMD genes in the HGMD database are illustrated as examples: [ c.265-463A > G ] is the shearing pathogenic site of a DMD gene recorded in the database, and other mutation forms [ c.265-463A > C ], [ c.265-463A > T ], [ c.265-463delA ] at the same coordinates are expanded into type IS mutation.
Through the process, high-risk pathogenic shearing site data are obtained through expansion, and statistics is carried out for standby.
4. Extension site screening.
And screening the obtained high-risk pathogenic mutation site data and high-risk pathogenic shearing site data, removing sites with mutation occurrence frequency higher than a preset threshold value, and combining the rest high-risk pathogenic mutation sites and high-risk pathogenic shearing sites with the reference data to form the pathogenic gene site database.
Specifically, after population frequency annotation of the extended sites, polymorphic sites (mainly class is and class III) can be excluded with a threshold of 5%.
For example, a point mutation c.293-13C > G (population frequency 0.2%) in the CYP21A2 gene intron affects cleavage, resulting in very severe 21-hydroxylase deficiency. And c.293-13C > A is a common polymorphic site in a crowd, the crowd frequency is up to 63%, and c.293-13C > T has no official statistical data of crowd frequency.
The base C at the position is a human genome reference sequence base, G is a pathogenic base recorded in an HGMD database, A and T are extended bases, and because A is a common polymorphic site in a crowd, pathogenicity of the polymorphic site can be eliminated, so that the polymorphic site can be eliminated, and only T is reserved as an extended risk pathogenic site.
For sites without official statistics of population frequency, and sites with population frequency below 5%, screening was performed using clinical information from the local sample library summarized by the inventors, using the following protocol:
1) Searching a sample with the position in a local sample library, if the number of the samples is less than 10, reserving the position, otherwise, performing the next step;
2) Clinical information of the samples is obtained, and if more than 1/3 of the clinical information of the samples is related to the gene in which the site is located, the site is reserved.
After the above treatment is removed and screened, the remaining high risk pathogenic mutation sites and high risk pathogenic cleavage sites are combined with the reference data obtained from the HGMD database in the first step, to form a pathogenic gene locus database in this embodiment.
5. Risk analysis of the extension site.
The pathogenicity of termination mutations is required to be as the case may be, termination mutations at different genes and at different exon positions may be at different risk of pathogenicity (termination mutations at certain exons of some genes are benign), while missense mutations are more detrimental.
The pathogenicity of the I type locus is more definite because the amino acid change is consistent with that in the database, and the IS type locus is the base change at the same coordinate of the shearing locus recorded in the database, and the pathogenicity is also more definite. The pathogenicity risks of class II and class III sites decrease in sequence. In practical applications, the judgment can be made according to the risk levels of several types of sites. The risk level is as follows from high to low: class I mutations, is mutations, class II mutations, class III mutations were reported.
6. Database listing site comparison.
And comparing the number of recorded mutation sites of the pathogenic gene locus database established by the expansion with the number of recorded mutation sites of the HGMD database, wherein the specific number is shown in the following table.
TABLE 1 site data alignment
| HGMD recording mutation count | 257,152 |
| Number of class I sites | 25,717 |
| Number of class is loci | 72,426 |
| Number of class II sites | 35,262 |
| Class III site count | 823,915 |
From the table, the proportion of the extended I, IS and II sites with higher risks to the total recorded site number of the HGMD exceeds 50%, and the number of the III sites with lower risks exceeds 3 times of the total recorded site number of the HGMD, so that the high-risk sites in the database are greatly enriched.
Example 2
An automated pathogenic gene analysis system comprising:
the data acquisition module is used for acquiring gene detection data of the sample to be detected;
the data analysis module Is used for substituting the gene detection data into the pathogenic gene locus database established in the embodiment 1 for comparison after bioinformatics analysis to obtain information of I type mutation, II type mutation, III type mutation and/or IS type mutation in the sample to be detected;
the judging and outputting module is used for outputting the site mutation information according to the risk level, wherein the risk level is sequentially as follows from high to low: class I mutations, class Is mutations, class II mutations, class III mutations.
Example 3
Sample data for detecting genes related to hereditary hearing loss were analyzed using the pathogenic gene automatic analysis system of example 2.
Mutations were detected in the conventional protocol for chr7:107350577A > G, which were retrieved in the HGMD raw data base as a risk site for the SLC26A4 gene [ c.2168A > G, p.His723Arg ]. The literature reports that the mutation is the most common mutation in east Asia deafness with enlarged vestibular aqueduct, but the SLC26A4 gene is recessive inheritance, and two pathogenic sites are needed for pathopoiesia.
After searching using the HGMD database extended in example 1, the patient was found to have a mutation of chr7:107323982G > A, which is also a causative gene locus of high risk pathogenicity, as follows.
As shown in Table 2, in the HGMD raw database, G > C and G > T at the chr7:107323982 position are both marked as pathogenic sites (DM markers), and G > T is considered to have a conflict in the pathogenic manner in different viewpoints, one viewpoint is considered to cause amino acid changes (later M markers) to cause diseases, and the other viewpoint is considered to cause shear changes (later S markers) to cause diseases; g > T at position 107323981 of chr7:5725 within the same codon range as chr7:107323982 is also marked as a pathogenic site.
Although the original database of HGMD does not contain the chr7:107323982G > A mutation of the patient in this case, the analysis of the database of pathogenic gene loci established by the example 1 shows that the chr7:107323982G > A is developed everywhere, one is class IS, and three is class III.
TABLE 2 analysis of pathogenic Gene loci
Note that: in the classification level, raw is the pathogenic site recorded in the original database, and raw_db is the information corresponding to the recorded site in the original database (HGMD). 1,8,9,10 sites are the recording sites of the HGMD original database, the other sites are expansion sites, 11,14,15,16 sites carried by patients in the present case, and the expansion sites are respectively expanded from the sites of 10,1,8,9. The codon at Gly334 of the gene is GGG, and the amino acid mutation type of the expansion site can be correspondingly shown according to the codon.
The above cases show that if only the HGMD original database is used, the chr7:107323982g > a mutation is easily omitted from the detection result of the patient, and because the position G > a is not a common mutation, various databases (including the thousand genome, dbSNP, HGMD, clinvar, etc.) are not recorded, and the site is easily found after analysis by using the pathogenic gene site database established in example 1, and the higher pathogenic risk is clarified, thereby reducing the detection difficulty and improving the diagnosis efficiency.
Example 4
Other cases were analyzed by using the disease causing gene automatic analysis system of example 2, and the disease causing gene locus database obtained in example 1 was evaluated by referring to the method of example 3. The results are as follows
Other missing report cases are exemplified by:
1. experiment No. NP15D3999 sample.
This sample was analyzed by the method of example 3, and the results are shown in tables 3 and 4 below.
TABLE 3 pathogenic Gene locus expansion
Note that: the codon at Thr1513 of the gene is ACT, and the amino acid mutation type of the expansion site can be correspondingly shown according to the codon.
TABLE 4 analysis of pathogenic loci of NP15D3999 samples
2. Experiment No. NP19S2603 sample.
This sample was analyzed by the method of example 3, and the results are shown in tables 5 and 6.
TABLE 5 pathogenic Gene locus expansion
Note that: the mutation site Is located in an intron, does not encode amino acids, but affects the cleavage and extends to an Is class mutation site.
TABLE 6 analysis of pathogenic gene loci of NP19S2603 samples
3. Test No. TP18D664 sample.
This sample was analyzed by the method of example 3, and the results are shown in tables 7 and 8 below.
TABLE 7 pathogenic Gene locus expansion
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Note that: the codon at Gly662 of the gene is GGG, and the amino acid mutation type of the expansion site can be correspondingly shown according to the codon.
TABLE 8 analysis of pathogenic gene loci of TP18D664 samples
4. Experiment No. NP20S768 sample.
This sample was analyzed by the method of example 3, and the results are shown in tables 9 and 10.
TABLE 9 pathogenic Gene locus expansion
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Note that: the codon at Phe306 of the gene is TTC, and the amino acid mutation type of the expansion site can be correspondingly shown according to the codon.
TABLE 10 analysis of pathogenic loci of sample NP20S768
In summary, in the conventional technology, the current interpretation of gene detection results is highly dependent on the pathogenicity sites recorded in the existing databases, which are the results of studies of gene data by humans for decades. However, in the actual genetic testing interpretation work, there are still a large number of suspicious mutation sites which are not recorded by the database, and the basic research on the suspicious mutation sites is impossible due to the timeliness of the clinical testing work.
By the method, a large number of site records with high pathogenic risk are obtained after the database is expanded, and the high-risk pathogenic sites can be rapidly positioned by carrying out matching analysis on the gene detection sites and the site records, so that the possibility of omission is reduced, and the accuracy and the efficiency of clinical interpretation work are greatly improved.
The technical features of the above-described embodiments may be arbitrarily combined, and all possible combinations of the technical features in the above-described embodiments are not described for brevity of description, however, as long as there is no contradiction between the combinations of the technical features, they should be considered as the scope of the description.
The above examples illustrate only a few embodiments of the invention, which are described in detail and are not to be construed as limiting the scope of the invention. It should be noted that it will be apparent to those skilled in the art that several variations and modifications can be made without departing from the spirit of the invention, which are all within the scope of the invention. Accordingly, the scope of protection of the present invention is to be determined by the appended claims.
Claims (9)
1. The method for establishing the pathogenic gene locus database is characterized by comprising the following steps of:
acquiring reference data: acquiring clinical verified pathogenic gene locus data information as reference data;
expansion yields mutation site data: acquiring pathogenic gene loci in the reference data due to amino acid change, expanding codons of amino acids of the loci, analyzing preset mutation generation conditions, obtaining high-risk pathogenic mutation locus data, and counting for later use;
expansion yields cleavage site data: acquiring pathogenic gene loci in the reference data due to change of the shearing loci, expanding other mutation forms of the loci to obtain high-risk pathogenic shearing locus data, and counting for later use;
extension site screening: and screening the obtained high-risk pathogenic mutation site data and high-risk pathogenic shearing site data, removing sites with mutation occurrence frequency higher than a preset threshold value, and combining the rest high-risk pathogenic mutation sites and high-risk pathogenic shearing sites with the reference data to form the pathogenic gene site database.
2. The method of claim 1, wherein the reference data is derived from HGMD database and/or ClinVar database.
3. The method of claim 1, wherein in the step of expanding the obtained mutation site data, the predetermined mutation generation conditions include the following three types:
the I type mutation is that the amino acid corresponding to the mutated codon is consistent with the reference data;
class II mutation to the post-mutation codon as the stop codon;
class III mutations are those in which the amino acid corresponding to the mutated codon is inconsistent with the reference data and is not a stop codon.
4. The method for creating a database of pathogenic loci according to claim 3, wherein the class I mutation is determined when the class I mutation and the class II mutation are satisfied at the same time.
5. The method of claim 3, wherein in the step of expanding the data of the cleavage site, the cleavage site Is specifically a mutation of a mutation site in the reference data to a nucleotide different from the reference data, i.e., an Is-type mutation.
6. The method of claim 1, wherein the predetermined threshold value in the extended site screening step is 5%.
7. The method according to claim 1, wherein in the extended site screening step, for sites having no definite occurrence frequency of mutation in the population, and for sites having occurrence frequency of mutation in the population lower than a predetermined threshold value obtained by screening, the following filtering is performed:
1) Searching a local sample library for a sample with the site, and if the number of samples is smaller than the preset number of samples, reserving the site as a high-risk pathogenic site; if the number of the samples is greater than or equal to the preset number of the samples, judging the sample to be confirmed, and carrying out the next step;
2) And acquiring the clinical information corresponding to the sample to be confirmed, if the clinical information of the sample exceeding the preset proportion is related to the gene function of the site, reserving the site as a high-risk pathogenic site, and if the clinical information of the sample less than or equal to the preset proportion is related to the gene function of the site, rejecting the site.
8. The method for creating a database of pathogenic loci according to claim 7, wherein the predetermined number of samples is 10 and the predetermined ratio is 1/3.
9. An automated pathogenic gene analysis system comprising:
the data acquisition module is used for acquiring gene detection data of the sample to be detected;
the data analysis module Is used for substituting the gene detection data into the pathogenic gene locus database of claim 5 for comparison after bioinformatics analysis to obtain information of I type mutation, II type mutation, III type mutation and/or IS type mutation in the sample to be detected;
the judging and outputting module is used for outputting the site mutation information according to the risk level, wherein the risk level is sequentially as follows from high to low: class I mutations, class Is mutations, class II mutations, class III mutations.
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